governance: keep repository root clean; remove marker file; implement repo detection via structure heuristic; update tests and system prompts/templates

collab/proposals/01-codexhelper.llm.md

@@ -15,8 +15,9 @@
 - Layout (project): `AGENTS.md`, `prompts/{project.md,style.md?}`, `prompts/_mode/`, `codex.yaml`, `codex.sh`, `runs/`.
 - Governance/Propagation: non-project-specific workflow changes get recorded in `prompts/global/` and seed AGENTS templates; proposal/plan updated so scaffolding includes them.
 - TDD Governance: adopt test-driven development with full unit/integration tests for all features in this repo and generated projects; tests written first and required for acceptance.
-- Zero Technical Debt: safety first; no technical debt; production-ready at all times; no deferring tests/docs/refactors; use sub-agents as needed.
+ - Zero Technical Debt: safety first; no technical debt; production-ready at all times; no deferring tests/docs/refactors; use sub-agents as needed.
  - Planning/Architecture Governance: plan ahead via Questions→Proposal→Plan; maintain a global architecture/module map; implement module-by-module; avoid refactors except when assumptions change and plans/docs are updated.
+  - Clean Root Governance: keep repo root minimal; organize assets under `docs/`, `templates/`, `collab/`, `prompts/`, `modes/`, `scripts/`, `meta/`.
 - Phase 1 acceptance:
   - new-mode creates mode skeleton
   - new-project scaffolds without overwrites
@@ -28,6 +29,7 @@
   - tests: unit/integration tests (bats) cover CLI flows and guardrails; TDD observed
   - zero debt: docs/tests included with every feature; no pending TODOs/deferrals; production-ready criteria met
   - planning: architecture/module map documented; module implementations follow approved plan with no unplanned refactors
+  - clean root: root remains minimal; scaffolding organizes assets under subdirectories
 \n+## Approval — Tick All That Apply
 
 - Subcommands approved: `new-project`, `run`, `new-mode` [ ]